Efficacy of endoscopic gastrojejunal bypass in obese Yucatan pigs: a comparative animal study

BACKGROUND

Natural orifice transluminal endoscopy surgery (NOTES) gastrojejunal anastomosis (GJA) with duodenal exclusion (DE) could be used as a less invasive alternative to surgical gastric bypass. The aim of this study was to compare the efficacy and safety of both methods for bariatric purpose.

METHODS

This was a prospective, experimental and comparative study on 27 obese living pigs, comparing 4 groups: GJA alone (group 1, G1), GJA + DE (group 2, G2), surgical gastric bypass (group 3, G3), control group (group 4, G4). GJA was endoscopically performed, using NOTES technic and LAMS, while DE was performed surgically for limb length selection. Animals were followed for 3 months. Primary outcome included technical success and weight change, while secondary endpoints included the rate of perioperative mortality and morbidity, histological anastomosis analysis and biological analysis.

RESULTS

Technical success was 100% in each intervention group. No death related to endoscopic procedures occurred in the endoscopic groups, while early mortality (< 1 month) was 57,1% in the surgical group, all due to anastomotic dehiscence. At 3 months, compared to baseline, mean weight change was + 3,1% in G1 (p = 0,46); -14,9% in G2 (p = 0,17); +5,6% in G3 (p = 0,38) and + 25% in G4 (p = 0,029). Histopathological analysis of endoscopic GJA showed complete fusion of different layers without leak or abscess.

CONCLUSIONS

Endoscopic GJA with DE provides the efficacy of bypass on weight control in an animal model. Next steps consist of the development of devices to perform exclusively endoscopically limb length selection and DE.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

An Explainable Machine-Learning Model for Compensatory Reserve Measurement: Methods for Feature Selection and the Effects of Subject Variability

Tracking vital signs accurately is critical for triaging a patient and ensuring timely therapeutic intervention. The patient's status is often clouded by compensatory mechanisms that can mask injury severity. The compensatory reserve measurement (CRM) is a triaging tool derived from an arterial waveform that has been shown to allow for earlier detection of hemorrhagic shock. However, the deep-learning artificial neural networks developed for its estimation do not explain how specific arterial waveform elements lead to predicting CRM due to the large number of parameters needed to tune these models. Alternatively, we investigate how classical machine-learning models driven by specific features extracted from the arterial waveform can be used to estimate CRM. More than 50 features were extracted from human arterial blood pressure data sets collected during simulated hypovolemic shock resulting from exposure to progressive levels of lower body negative pressure. A bagged decision tree design using the ten most significant features was selected as optimal for CRM estimation. This resulted in an average root mean squared error in all test data of 0.171, similar to the error for a deep-learning CRM algorithm at 0.159. By separating the dataset into sub-groups based on the severity of simulated hypovolemic shock withstood, large subject variability was observed, and the key features identified for these sub-groups differed. This methodology could allow for the identification of unique features and machine-learning models to differentiate individuals with good compensatory mechanisms against hypovolemia from those that might be poor compensators, leading to improved triage of trauma patients and ultimately enhancing military and emergency medicine.

Evaluating the Performance of a Nonelectronic, Versatile Oxygenating Perfusion System across Viscosities Representative of Clinical Perfusion Solutions Used for Organ Preservation

Introduction: On the United States' Organ Transplantation Waitlist, approximately 17 people die each day waiting for an organ. The situation continues to deteriorate as the discrepancy between harvested organs and the number of patients in need is increasing. Static cold storage is the clinical standard method for preserving a harvested organ but is associated with several drawbacks. Machine perfusion of an organ has been shown to improve preservation quality as well as preservation time over static cold storage. While there are machine perfusion devices clinically available, they are costly and limited to specific organs and preservation solutions. This study presents a versatile oxygenating perfusion system (VOPS) that supplies oxygen and pulsatile perfusion. Materials and Methods: Experiments evaluated the system's performance with a human kidney mimicking hydraulic analog using multiple compressed oxygen supply pressures and aqueous solutions with viscosities ranging from 1 to 6.5 cP, which simulated viscosities of commonly used organ preservation solutions. Results and Conclusions: The VOPS produced mean flow rates ranging from 0.6 to 28.2 mL/min and perfusion pressures from 4.8 to 96.8 mmHg, which successfully achieved the desired perfusion parameters for human kidneys. This work provides evidence that the VOPS described herein has the versatility to perfuse organs using many of the clinically available preservation solutions.

Training Ultrasound Image Classification Deep-Learning Algorithms for Pneumothorax Detection Using a Synthetic Tissue Phantom Apparatus

Ultrasound (US) imaging is a critical tool in emergency and military medicine because of its portability and immediate nature. However, proper image interpretation requires skill, limiting its utility in remote applications for conditions such as pneumothorax (PTX) which requires rapid intervention. Artificial intelligence has the potential to automate ultrasound image analysis for various pathophysiological conditions. Training models require large data sets and a means of troubleshooting in real-time for ultrasound integration deployment, and they also require large animal models or clinical testing. Here, we detail the development of a dynamic synthetic tissue phantom model for PTX and its use in training image classification algorithms. The model comprises a synthetic gelatin phantom cast in a custom 3D-printed rib mold and a lung mimicking phantom. When compared to PTX images acquired in swine, images from the phantom were similar in both PTX negative and positive mimicking scenarios. We then used a deep learning image classification algorithm, which we previously developed for shrapnel detection, to accurately predict the presence of PTX in swine images by only training on phantom image sets, highlighting the utility for a tissue phantom for AI applications.

Development of a Modular Tissue Phantom for Evaluating Vascular Access Devices

Central vascular access (CVA) may be critical for trauma care and stabilizing the casualty. However, it requires skilled personnel, often unavailable during remote medical situations and combat casualty care scenarios. Automated CVA medical devices have the potential to make life-saving therapeutics available in these resource-limited scenarios, but they must be properly designed. Unfortunately, currently available tissue phantoms are inadequate for this use, resulting in delayed product development. Here, we present a tissue phantom that is modular in design, allowing for adjustable flow rate, circulating fluid pressure, vessel diameter, and vessel positions. The phantom consists of a gelatin cast using a 3D-printed mold with inserts representing vessels and bone locations. These removable inserts allow for tubing insertion which can mimic normal and hypovolemic flow, as well as pressure and vessel diameters. Trauma to the vessel wall is assessed using quantification of leak rates from the tubing after removal from the model. Lastly, the phantom can be adjusted to swine or human anatomy, including modeling the entire neurovascular bundle. Overall, this model can better recreate severe hypovolemic trauma cases and subject variability than commercial CVA trainers and may potentially accelerate automated CVA device development.

Fibrillin-1 mutant mouse captures defining features of human primary open glaucoma including anomalous aqueous humor TGF beta-2

Primary open angle glaucoma (POAG) features an optic neuropathy, elevated aqueous humor (AH) TGFβ2, and major risk factors of central corneal thickness (CCT), increasing age and intraocular pressure (IOP). We examined Tight skin (Tsk) mice to see if mutation of fibrillin-1, a repository for latent TGFβ, is associated with characteristics of human POAG. We measured: CCT by ocular coherence tomography (OCT); IOP; retinal ganglion cell (RGC) and optic nerve axon counts by microscopic techniques; visual electrophysiologic scotopic threshold responses (STR) and pattern electroretinogram (PERG); and AH TGFβ2 levels and activity by ELISA and MINK epithelial cell-based assays respectively. Tsk mice had open anterior chamber angles and compared with age-matched wild type (WT) mice: 23% thinner CCT (p < 0.003); IOP that was higher (p < 0.0001), more asymmetric (p = 0.047), rose with age (p = 0.04) and had a POAG-like frequency distribution. Tsk mice also had RGCs that were fewer (p < 0.04), declined with age (p = 0.0003) and showed increased apoptosis and glial activity; fewer optic nerve axons (p = 0.02); abnormal axons and glia; reduced STR (p < 0.002) and PERG (p < 0.007) visual responses; and higher AH TGFβ2 levels (p = 0.0002) and activity (p = 1E-11) especially with age. Tsk mice showed defining features of POAG, implicating aberrant fibrillin-1 homeostasis as a pathogenic contributor to emergence of a POAG phenotype.

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research

Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1 and RefSeq2 launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref. 3) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.

Diversity and enzymatic potential of thermophilic bacteria associated with terrestrial hot springs in Algeria

This study aims to determine the diversity of culturable thermophilic bacteria isolated from eight terrestrial hot springs in Northeastern of Algeria using the conventional methods, SDS-PAGE fingerprinting of whole-cell proteins and 16S rRNA gene sequencing. In addition, their hydrolytic enzyme activities were also investigated. A total of 293 strains were isolated from the hot springs' water and sediment using different culture media. Overall, five distinct bacterial groups were characterized by whole-cell protein pattern analysis. Based on the 16S rRNA gene sequencing of 100 selected strains, the isolates were assigned to the following three major phyla: Firmicutes (93%), Deinococcus-Thermus (5%), and Actinobacteria (2%), which included 27 distinct species belonging to 12 different phylotypes, Aeribacillus, Aneurinibacillus, Anoxybacillus, Bacillus, Brevibacillus, Geobacillus, Laceyella, Meiothermus, Saccharomonospora, Thermoactinomyces, Thermobifida, and Thermus. The screening for nine extracellular enzymes showed that 65.87% of the isolates presented at least five types of enzyme activities, and 6.48% of strains combined all tested enzymes (amylase, cellulase, pectinase, esculinase, protease, gelatinase, lipase, lecithinase, and nuclease). It was found that Bacillus, Anoxybacillus, Aeribacillus, and Aneurinibacillus were the genera showing the highest activities. Likewise, the study showed an abundant and diverse thermophilic community with novel taxa presenting a promising source of thermozymes with important biotechnological applications. This study showed that a combined identification method using SDS-PAGE profiles of whole-cell proteins and subsequent 16S rRNA gene sequence analysis could successfully differentiate thermophilic bacteria from Algerian hot springs.

Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons

BACKGROUND

Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences.

RESULTS

Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.

CONCLUSIONS

This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date. The complete annotation has been integrated into the GENCODE reference gene set, for immediate availability to the research community.

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community.

GPR158 in the Visual System: Homeostatic Role in Regulation of Intraocular Pressure

Purpose: GPR158 is a newly characterized family C G-protein-coupled receptor, previously identified in functional screens linked with biological stress, including one for susceptibility to ocular hypertension/glaucoma induced by glucocorticoid stress hormones. In this study, we investigated GPR158 function in the visual system. Methods: Gene expression and protein immunolocalization analyses were performed in mouse and human brain and eye to identify tissues where GPR158 might function. Gene expression was perturbed in mice, and in cultures of human trabecular meshwork cells of the aqueous outflow pathway, to investigate function and mechanism. Results: GPR158 is highly expressed in the brain, and in this study, we show prominent expression specifically in the visual center of the cerebral cortex. Expression was also observed in the eye, including photoreceptors, ganglion cells, and trabecular meshwork. Protein was also localized to the outer plexiform layer of the neural retina. Gpr158 deficiency in knockout (KO) mice conferred short-term protection against the intraocular pressure increase that occurred with aging, but this was reversed over time. Most strikingly, the pressure lowering effect of the acute stress hormone, epinephrine, was negated in KO mice. In contrast, no disruption of the electroretinogram was observed. Gene overexpression in cell cultures enhanced cAMP production in response to epinephrine, suggesting a mechanism for intraocular pressure regulation. Overexpression also increased survival of cells subjected to oxidative stress linked to ocular hypertension, associated with TP53 pathway activation. Conclusions: These findings implicate GPR158 as a homeostatic regulator of intraocular pressure and suggest GPR158 could be a pharmacological target for managing ocular hypertension.

Interaction between supplemental zinc oxide and zilpaterol hydrochloride on growth performance, carcass traits, and blood metabolites in feedlot steers

Interactive effects of supplemental Zn and zilpaterol hydrochloride (ZH) were evaluated in feedlot steers ( = 40; 652 kg ± 14 initial BW) to determine their impact on feedlot performance, blood constituents, and carcass traits. The study was conducted as a randomized complete block design with a 2 × 2 factorial treatment arrangement. Steers were blocked by BW and randomly assigned to treatments. Factors consisted of supplemental Zn (60 or 300 mg/kg diet DM) and ZH (0 or 8.33 mg/kg) in the diets. For diets supplemented with 300 mg Zn/kg DM, 60 mg Zn/kg was supplemented as zinc sulfate and 240 mg Zn/kg was supplemented as zinc oxide, and the diet was fed for 24 d. Zilpaterol hydrochloride was fed for 21 d followed by a 3-d withdrawal. Cattle were housed in partially covered individual feeding pens equipped with automatic waterers and fence-line feed bunks and were fed once daily for ad libitum intake. Plasma samples were collected on d 0 and 21 to assess changes in Zn, plasma urea nitrogen (PUN), glucose, and lactate concentrations, and serum samples were collected on d 21 to assess IGF-1 concentration. On d 25, cattle were weighed and transported 450 km to a commercial abattoir for harvest; HCW and incidence of liver abscesses were recorded. Carcass data were collected after 36 h of refrigeration. Data were analyzed as a mixed model with Zn, ZH, and Zn × ZH as fixed effects; block as a random effect; and steer as the experimental unit. No interaction or effects of Zn or ZH were observed for IGF-1 concentration, plasma glucose, or lactate concentrations ( ≥ 0.25). No interaction between Zn and ZH was observed for PUN concentration, but PUN decreased with ZH ( < 0.01). There were no effects of ZH or Zn on ADG, DMI, final BW, feed efficiency, HCW, back fat, KPH, quality grade, or incidence of liver abscesses ( > 0.05). Zinc supplementation tended ( = 0.08) to improve the proportion of carcasses grading USDA Choice. Feeding ZH decreased yield grade ( = 0.05) and tended to increase LM area ( = 0.07). In conclusion, increasing dietary concentrations of Zn does not impact response to ZH, but feeding ZH altered circulating concentrations of PUN.

Effect of Brahman genetics on myofibrillar protein degradation, collagen crosslinking, and tenderness of the longissimus lumborum

The objective of this study was to examine the effect of percent Brahman genetics on Warner-Bratzler shear force (WBSF), desmin and troponin-T (TnT) degradation, hydroxylysyl pyridinoline (HP) crosslink content, and perimysial collagen melting temperature. Steers ( = 131) produced in 2012 and 2013 were harvested at 1.27 cm of visual s.c. back fat thickness. Steers were divided into 4 genetic categories consisting of steers that contained 6/32 or less Brahman genetics, 12/32 Brahman genetics, 14/32 to 18/32 Brahman genetics, and 23/32 to 32/32 Brahman genetics. Twenty-four hours after harvest, a 7.62-cm piece of the longissimus lumborum beginning at the 13th rib was collected and aged for 14 d. Following aging, three 2.54-cm steaks were cut for WBSF, trained sensory panel, and laboratory analyses. Laboratory analyses steaks were used to determine protein degradation, HP crosslink analysis, and perimysial collagen melting temperature. Data were analyzed using a polynomial regression for unequally spaced treatments. As the percent Brahman genetics increased, WBSF increased (linear, = 0.01). As percent Brahman genetics increased, tenderness score decreased (less tender) and connective tissue score increased (more connective tissue; linear, = 0.01). As the percentage of Brahman genetics increased, the amount of degraded desmin (38 kDa) and TnT (34 and 30 kDa) decreased (linear, < 0.03) whereas the amount of immunoreactive 36 kDa TnT increased (linear, = 0.04). Percent Brahman genetics had no effect ( = 0.14) on HP crosslink content but did tend to increase ( = 0.07) perimysial collagen melting temperature as the percent Brahman increased. The percentage of Brahman genetic influence was positively correlated to WBSF ( = 0.25), 36 kDa immunoreactive TnT ( = 0.26), and perimysial collagen melting temperature ( = 0.25, = 0.01). Sensory panel tenderness ( = -0.44), juiciness ( = -0.26), and connective tissue scores ( = -0.63); 38 kDa degraded desmin ( = -0.34), 34 ( = -0.36) and 30 kDa degraded TnT ( = -0.29); and HP collagen crosslinks ( = -0.20) were negatively correlated to percent Brahman genetic influence ( < 0.03). Increasing Brahman genetic influence in steers negatively affects tenderness, partially through a reduction in degradation of desmin and TnT. Although HP collagen crosslinks are unaffected by Brahman genetics, a tendency for increased perimysium melting temperature indicates that other collagen-stabilizing crosslinks may be affected.

Interactive effects of supplemental Zn sulfate and ractopamine hydrochloride on growth performance, carcass traits, and plasma urea nitrogen in feedlot heifers

Interactive effects of supplemental Zn and ractopamine hydrochloride (RH) were evaluated using 156 crossbred heifers (initial BW = 527 kg ± 6.61; gross BW × 0.96) to determine the impact on feedlot performance, plasma urea nitrogen (PUN), and carcass characteristics. The study was conducted as a randomized complete block design with a 2 × 2 factorial arrangement of treatments. Factors consisted of 1) 30 or 100 mg supplemental Zn/kg diet DM (30Zn or 100Zn) as Zn sulfate and 2) 0 or 200 mg RH/heifer daily. Heifers were blocked by BW and assigned randomly within block to treatments for a 43-d trial. Heifers were housed in partially covered feeding pens (3 heifers/pen; 13 pens/treatment) and provided ad libitum access to feed. Ractopamine hydrochloride was fed for 42 d and removed from the diet until cattle were harvested on d 43. Zinc treatments were fed until harvest. Plasma samples were collected on d 0 and 36 to assess changes in plasma Zn and PUN. On d 43, heifers were weighed, then transported to a commercial abattoir where HCW and incidence of liver abscesses were recorded. Carcass data were collected after 32 h of refrigeration. No Zn × RH interactions were observed for plasma Zn or PUN ( ≥ 0.58); however, there was a tendency for a RH × day interaction for PUN ( = 0.08). Supplementing 100Zn resulted in increased plasma Zn ( = 0.02) compared to 30Zn. No RH × Zn interactions were observed for feedlot performance ( ≥ 0.24). Final BW and ADG increased with RH supplementation ( ≤ 0.02), but DMI was not affected ( = 0.63); thus, feed efficiency improved ( < 0.01) when heifers were fed RH. Supplementing 100Zn tended to reduce ADG ( = 0.07) but did not affect other measures of feedlot performance ( ≥ 0.12). Zinc × RH interactions were observed for LM area and yield grade ( ≤ 0.01); LM area decreased and yield grade increased when heifers were supplemented 100Zn with no RH compared to other treatments. A tendency for a Zn × RH interaction was observed for dressed yield ( = 0.08), but no other interactions or effects of Zn were detected for carcass traits ( ≥ 0.11). Supplementing RH increased HCW ( = 0.03) but did not affect other carcass traits ( ≥ 0.13). In conclusion, supplemental Zn had little impact on feedlot performance or PUN concentration but may alter muscle and fat deposition when fed in conjunction with RH.

Deep tissue analysis of distal aqueous drainage structures and contractile features

Outflow resistance in the aqueous drainage tract distal to trabecular meshwork is potentially an important determinant of intraocular pressure and success of trabecular bypass glaucoma surgeries. It is unclear how distal resistance is modulated. We sought to establish: (a) multimodal 2-photon deep tissue imaging and 3-dimensional analysis of the distal aqueous drainage tract (DT) in transgenic mice in vivo and ex vivo; (b) criteria for distinguishing the DT from blood and lymphatic vessels; and (c) presence of a DT wall organization capable of contractility. DT lumen appeared as scleral collagen second harmonic generation signal voids that could be traced back to Schlemm's canal. DT endothelium was Prox1-positive, CD31-positive and LYVE-1-negative, bearing a different molecular signature from blood and true lymphatic vessels. DT walls showed prominent filamentous actin (F-actin) labeling reflecting cells in a contracted state. F-actin co-localized with mesenchymal smooth muscle epitopes of alpha-smooth muscle actin, caldesmon and calponin, which localized adjacent and external to the endothelium. Our findings support a DT wall organization resembling that of blood vessels. This reflects a capacity to contract and support dynamic alteration of DT caliber and resistance analogous to the role of blood vessel tone in regulating blood flow.

Total Outflow Facility in Live C57BL/6 Mice of Different Age

Purpose

To characterize total outflow facility across the live adult mouse lifespan as a reference for mouse glaucoma studies and the common C57BL/6 background strain.

Methods

Microperfusion was performed by single-needle cannulation and feedback-controlled coupling of pressure and flow to maintain a constant pressure in the anterior chambers of live C57BL/6NCrl mice aged 3-4 months (n = 17), 6-9 months (n = 10), and 23-27 months (n = 12). This mouse age range represented an equivalent human age range of young adult to elderly. We characterized the following across age groups in vivo: (1) outflow facility based on constant pressure perfusion in a pressure range of 15-35 mm Hg, (2) perfusion flow rates, and (3) anterior segment tissue histology after perfusion. Thirty-nine live mice underwent perfusion.

Results

Pressure-flow rate functions were consistently linear for all age groups (all R ² > 0.96). Total outflow facility in mice aged 3-4, 6-9, and 23-27 months was 0.0066, 0.0064, and 0.0077 μL/min/mm Hg, respectively. Facility was not significantly different between age groups (all p > 0.4). The groups had closely overlapping frequency distribution profiles with right-sided tails. Post hoc estimates indicated that group facility differences of at least 50% would have been detectable, with this limit set mainly by inherent variability in the strain. A trend toward higher perfusion flow rates was seen in older mice aged 23-27 months, but this was not significantly different from that of mice aged 3-4 months or 6-9 months (p > 0.2). No histological disruption or difference in iridocorneal angle or drainage tissue structure was seen following perfusion in the different age groups.

Conclusion

We did not find a significant difference in total outflow facility between different age groups across the live C57BL/6 mouse adult lifespan, agreeing with some human studies. The possibility that more subtle differences might exist ought to be judged with respect to the heterogeneity in facility at different ages. Our findings provide reference data for live perfusion studies pertaining to glaucoma involving the C57BL/6 strain.

Software for improved field surveys of nesting marine turtles

Field data are still recorded on paper in many worldwide beach surveys of nesting marine turtles. The data must be subsequently transferred into an electronic database, and this can introduce errors in the dataset. To minimize such errors, the "Turtles" software was developed and piloted to record field data by one software user accompanying one Tortuguero in Akumal beaches, Quintana Roo, Mexico, from June 1^st to July 31^st during the night patrols. Comparisons were made between exported data from the software with the paper forms entered into a database (henceforth traditional). Preliminary assessment indicated that the software user tended to record a greater amount of metrics (i.e., an average of 18.3 fields ± 5.4 sd vs. 8.6 fields ± 2.1 sd recorded by the traditional method). The traditional method introduce three types of "errors" into a dataset: missing values in relevant fields (40.1%), different answers for the same value (9.8%), and inconsistent data (0.9%). Only 5.8% of these (missing values) were found with the software methodology. Although only tested by a single user, the software may suggest increased efficacy and warrants further examination to accurately assess the merit of replacing traditional methods of data recording for beach monitoring programmes.

G-POEM with antro-pyloromyotomy for the treatment of refractory gastroparesis: mid-term follow-up and factors predicting outcome

BACKGROUND

Gastric peroral endoscopic pyloromyotomy (G-POEM) was introduced for treating refractory gastroparesis.

AIM

To present a series of patients focussed on clinical mid-term efficacy and predictive outcomes factors.

METHODS

This was a single centre study of 29 patients operated on between January 2014 and April 2016, with disturbed gastric emptying scintigraphy (GES) and/or elevated Gastroparesis Cardinal Symptoms Index (GCSI). The procedures were performed as previously described. The primary endpoint was the efficacy at 3 and 6 months, based on GCSI and symptoms. The secondary endpoints were GES evolution, procedure reproducibility and safety, and identification of predictive factors for success.

RESULTS

There were 10 men, 19 women (mean age 52.8±18). The technical success rate was 100% (average 47 minutes). There were two complications managed conservatively: one bleeding and one abscess. The median follow-up was 10±6.4 months. The clinical success rate was 79% at 3 months, 69% at 6 months, with a significant decrease in the mean GCSI compared to pre-operatively (3.3±0.9 vs 1±1.2 and 1.1±0.9 respectively). The GES (n=23) normalised in 70% of cases, with a significant improvement of the mean half emptying time and retention at 2 hours, and a discordance in 21% of the cases. In univariate analysis, diabetes and female gender were significantly associated with risk of failure, but not confirmed in multivariate analysis.

CONCLUSIONS

The mid-term efficacy of G-POEM reaches 70% at 6 months. The procedure remains reproducible and safe. Diabetes and female gender were predictive of failure.

Effects of yeast combined with chromium propionate on growth performance and carcass quality of finishing steers

A combination of yeast and chromium propionate (Y+Cr) was added to the diets of crossbred finishing steers ( = 504; 402 kg ± 5.76 initial BW) to evaluate impact on feedlot performance and carcass traits. We hypothesized supplementation of Y+Cr would increase growth of feedlot steers. Steers with initial plasma glucose concentrations ≤6.0 m were stratified by initial BW and randomly allocated, within strata, to receive 0 (control) or 3.3 g/d Y+Cr. Steers were further divided into heavy and light weight blocks with 6 pens/diet within each weight block. Cattle were housed in dirt-surfaced pens with 21 steers/pen and had ad libitum access to feed. Body weights were measured at 21-d intervals. Blood samples were collected on d 49 and 94 from a subset of steers (5/pen) for analyses of plasma glucose and lactate concentrations. At the end of the finishing phase, animals were weighed and transported 450 km to an abattoir in Holcomb, KS. Severity of liver abscesses and HCW were collected the day of harvest, and after 36 h of refrigeration, USDA yield and quality grades, LM area, and 12th rib subcutaneous fat thickness were determined. There were no treatment × time × weight block interactions ( > 0.05) and no treatment × block interaction for ADG, DMI, or final BW ( ≥ 0.06), but a treatment × block interaction ( = 0.03) was observed for G:F, in which control, light cattle had poorer efficiency compared with other groups. Treatment × weight group interactions were observed for overall yield grade and carcasses that graded yield grade 1 ( ≤ 0.04). Light steers supplemented with Y+Cr had decreased overall yield grade and increased percentage of carcasses grading yield grade 1 compared with their control counterparts, with no differences observed for heavy steers. Regardless of weight group, a greater percentage of carcasses from steers supplemented with Y+Cr graded yield grade 2 ( = 0.03) and fewer carcasses from steers supplemented Y+Cr graded yield grade 3 ( < 0.01) than control steers. No interactions or effects of treatment were detected for other carcass measurements ( ≥ 0.07). There were no treatment × weight group interactions or effects of treatment for plasma glucose or lactate concentrations on d 49 or 94 ( > 0.10). Overall, yeast in combination with chromium propionate may improve feed efficiency and decrease yield grade of light cattle but had no effect on remaining carcass traits and blood constituents.

Use of electromyography to detect muscle exhaustion in finishing barrows fed ractopamine HCl

The objectives of this study were to determine the effects of dietary ractopamine HCl (RAC) on muscle fiber characteristics and electromyography (EMG) measures of finishing barrow exhaustion when barrows were subjected to increased levels of activity. Barrows ( = 34; 92 ± 2 kg initial BW) were assigned to 1 of 2 treatments: a conventional swine finishing diet containing 0 mg/kg ractopamine HCl (CON) or a diet formulated to meet the requirements of finishing barrows fed 10 mg/kg RAC (RAC+). After 32 d on feed, barrows were individually moved around a track at 0.79 m/s until subjectively exhausted. Wireless EMG sensors were affixed to the deltoideus (DT), triceps brachii lateral head (TLH), tensor fasciae latae (TFL), and semitendinosus (ST) muscles to measure median power frequency (MdPF) and root mean square (RMS) as indicators of action potential conduction velocity and muscle fiber recruitment, respectively. After harvest, samples of each muscle were collected for fiber type, succinate dehydrogenase (SDH), and capillary density analysis. Speed was not different ( = 0.82) between treatments, but RAC+ barrows reached subjective exhaustion earlier and covered less distance than CON barrows ( < 0.01). There were no treatment × muscle interactions or treatment effects for end-point MdPF values ( > 0.29). There was a treatment × muscle interaction ( = 0.04) for end-point RMS values. The RAC diet did not change end-point RMS values in the DT or TLH ( > 0.37); however, the diet tended to decrease and increase end-point RMS in the ST and TFL, respectively ( < 0.07). There were no treatment × muscle interactions for fiber type, SDH, or capillary density measures ( > 0.10). Muscles of RAC+ barrows tended to have less type I fibers and more capillaries per fiber ( < 0.07). Type I and IIA fibers of RAC+ barrows were larger ( < 0.07). Compared with all other muscles, the ST had more ( < 0.01) type IIB fibers and larger type I, IIA, and IIX fibers ( < 0.01). Type I, IIA, and IIX fibers of the ST also contained less SDH compared with the other muscles ( < 0.01). Barrows fed a RAC diet had increased time to subjective exhaustion due to loss of active muscle fibers in the ST, possibly due to fibers being larger and less oxidative in metabolism. Size increases in type I and IIA fibers with no change in oxidative capacity could also contribute to early exhaustion of RAC+ barrows. Overall, EMG technology can measure real-time muscle fiber loss to help explain subjective exhaustion in barrows.

The effect of branding on consumer palatability ratings of beef strip loin steaks

The objective of this study was to determine the influence of knowing the brand or USDA grade on consumer palatability ratings of beef strip loin steaks. Strip loins were selected to represent 5 USDA grades and brands, USDA Select, Choice, Prime, Certified Angus Beef (CAB; upper 2/3 Choice), and Select, from carcasses of cattle classified as Angus on the basis of phenotype. After 21 d of aging, 2.5-cm-thick steaks were cut, consecutively cut steaks were paired for consumer evaluation. Consumer panelists ( = 112) evaluated samples for tenderness, juiciness, flavor liking, and overall liking. Additionally, consumers rated each palatability trait as either acceptable or unacceptable. Samples were fed in 2 rounds on the same day: blind and informed testing. In the first round, blind testing, consumers were served 1 sample from each treatment, with no product information provided. In the second round, consumers were informed of the brand or quality grade prior to sampling. During blind testing, CAB rated similar ( > 0.05) to Choice for all palatability traits; however, CAB rated greater ( < 0.05) than Choice for all traits during informed testing. Additionally, Angus Select and Select were rated similar > 0.05) for all traits when tested blind, but Angus Select was rated greater ( < 0.05) than Select for flavor and overall liking when brand was declared. When comparing blind and informed ratings, Angus Select and CAB had greater ( < 0.05) ratings for juiciness, flavor liking, and overall liking, and Prime had increased ( < 0.05) ratings for flavor liking and overall liking because of brand disclosure. However, ratings for Choice and Select samples were unaffected ( > 0.05) when brand was disclosed. Brand knowledge increased ( < 0.05) the percentage of Prime samples rated as acceptable for flavor and the percentage of Angus Select samples rated as acceptable for flavor and overall liking. Conversely, there was no difference ( > 0.05) in the percentage of Choice and Select samples rated as acceptable for all palatability traits. These data indicate that Prime, CAB, and Angus Select steaks receive an increase in consumer palatability perception, or "brand lift," which does not occur for Choice and Select beef.

Determination of the effect of brand and product identification on consumer palatability ratings of ground beef patties

The objective of this study was to determine the effect of brand and product identification on consumer palatability ratings of ground beef patties. Six treatments were used in the study: 90/10 Certified Angus Beef (CAB) ground sirloin, 90/10 ground beef, 80/20 CAB ground chuck, 80/20 ground chuck, 80/20 ground beef, and 73/27 CAB ground beef. Ground beef was processed into 151.2-g patties using a patty former with 2 consecutively formed patties assigned to blind consumer testing and the following 2 assigned to informed testing. Following cooking to 74°C, patties were cut into quarters and served to consumers. Consumers ( = 112) evaluated samples in 2 rounds for tenderness, juiciness, flavor liking, texture liking, and overall liking. Each trait was also rated as either acceptable or unacceptable. In the first round of testing, samples were blind evaluated, with no information about the treatments provided to consumers, but in the second round, product type and brand were disclosed prior to sample evaluation. Additionally, texture profile and shear force analyses were performed on patties from each treatment. Few differences were observed for palatability traits during blind consumer testing; however, during informed testing, 90/10 CAB ground sirloin was rated greatest ( < 0.05) for all palatability traits other than juiciness. Also, 90/10 CAB ground sirloin had increased ( < 0.05; (consumer informed score - consumer blind score)/consumer blind score) ratings for tenderness (17.4%), juiciness (36.5%), flavor liking (23.3%), texture liking (18.2%), and overall liking (24.7%) due to brand disclosure. Increased ( < 0.05) ratings were found for CAB products for multiple traits due to treatment disclosure, whereas the only non-CAB-branded product that received increased ( < 0.05) ratings during informed testing was 90/10 ground beef for tenderness and juiciness. Texture results indicated that decreased fat level increased hardness, cohesiveness, gumminess, and chewiness. These results indicate that when sampling ground beef without brand and product information, few consumers find differences in eating quality among ground beef treatments; however, when consumers are aware of the brand, fat level, and subprimal blend prior to sampling, these factors have a large impact on consumer eating satisfaction.

Feeding microalgae meal (All-G Rich; CCAP 4087/2) to beef heifers. I: Effects on longissimus lumborum steak color and palatibility

The objective of this study was to examine effects of 4 levels of microalgae meal (All-G Rich, CCAP 4087/2; Alltech Inc., Nicholasville, KY) supplementation to the diet of finishing heifers on longissimus lumborum (LL) steak PUFA content, beef palatability, and color stability. Crossbred heifers ( = 288; 452 ± 23 kg initial BW) were allocated to pens (36 pens and 8 heifers/pen), stratified by initial pen BW (3,612 ± 177 kg), and randomly assigned within strata to 1 of 4 treatments: 0, 50, 100, and 150 g·heifer·d of microalgae meal. After 89 d of feeding, cattle were harvested and LL were collected for determination of fatty acid composition and Warner-Bratzler shear force (WBSF), trained sensory panel evaluation, and 7-d retail color stability and lipid oxidation analyses. Feeding microalgae meal to heifers increased (quadratic, < 0.01) the content of 22:6-3 and increased (linear, < 0.01) the content of 20:5-3. Feeding increasing levels of microalgae meal did not impact total SFA or MUFA ( > 0.25) but tended ( = 0.10) to increase total PUFA in a quadratic manner ( = 0.03). Total omega-6 PUFA decreased (linear, = 0.01) and total omega-3 PUFA increased (quadratic, < 0.01) as microalgae meal level increased in the diet, which caused a decrease (quadratic, < 0.01) in the omega-6:omega-3 fatty acid ratio. Feeding microalgae meal did not affect WBSF values or sensory panel evaluation of tenderness, juiciness, or beef flavor scores ( > 0.16); however, off-flavor intensity increased with increasing concentration of microalgae meal in the diet (quadratic, < 0.01). From d 5 through 7 of retail display, steaks from heifers fed microalgae meal had a reduced a* value and oxymyoglobin surface percentage, with simultaneous increased surface metmyoglobin formation (quadratic, < 0.01). Lipid oxidation analysis indicated that at d 0 and 7 of display, as the concentration of microalgae meal increased in the diet, the level of oxidation increased (quadratic, < 0.01). Muscle fiber type percentage or size was not influenced by the inclusion of microalgae meal in diets ( > 0.19); therefore, the negative effects of microalgae on color stability were not due to fiber metabolism differences. Feeding microalgae meal to finishing heifers improves PUFA content of beef within the LL, but there are adverse effects on flavor and color stability.

Feeding microalgae meal (All-G Rich; CCAP 4067/2) to beef heifers. II: Effects on ground beef color and palatability

The objective of this study was to examine the effects of feeding microalgae meal (All-G Rich, CCAP 4087/2; Alltech Inc., Nicholasville, KY) to finishing heifers on 85% lean and 15% fat (85/15) ground beef PUFA content, palatability, and color stability. Crossbred heifers ( = 288; 452 ± 23 kg initial BW) were allocated to pens (36 pens and 8 heifers/pen), stratified by initial pen BW (3,612 ± 177 kg), and randomly assigned within strata to 1 of 4 treatments: 0, 50, 100, and 150 g·heifer·d of microalgae meal. After 89 d of feeding, a subset of heifers (3/pen) was harvested and the rectus femoris, vastus lateralis, vastus medialis, and vastus intermedius were collected for processing into ground beef. At 42 d postmortem, 85/15 ground beef was formulated and formed into 112-g patties and fatty acid composition, subjective palatability, and 96-h retail color stability analyses were conducted. Increasing dietary microalgae meal concentration increased ground beef 20:5-3 and 22:6-3 fatty acids (quadratic, < 0.01). There was a treatment × hour interaction for all color attributes ( < 0.01). On d 0, microalgae tended ( = 0.08) to decrease L*, but patties had similar L* values the remainder of display ( > 0.12). Feeding microalgae meal affected ( = 0.02) b* at 24 h and decreased (linear, = 0.08) b* at 48 h. From h 0 to 36 of display, microalgae affected redness of patties ( < 0.02), and from 48 to 72 h, microalgae meal decreased a* value (linear, < 0.04). Microalgae meal did not impact sensory panel firmness, overall tenderness, or juiciness scores ( > 0.20) but tended to affect ( = 0.10) cohesiveness scores. As the amount of microalgae meal fed to heifers increased, beef flavor intensity decreased (linear, < 0.01) and off-flavor intensity increased (quadratic, < 0.05). Surface oxymyoglobin and metmyoglobin were impacted by microalgae meal from 12 to 36 h of display ( < 0.01). From 48 to 84 h of display, feeding microalgae meal to heifers decreased (linear, < 0.09) surface oxymyoglobin and increased (linear, < 0.02) surface metmyoglobin of patties. Although feeding microalgae meal to heifers increases the PUFA content of 85/15 ground beef, there are undesirable effects on flavor and color stability.

Induction of cellular proliferation in a human astrocytoma cell line by a Trypanosoma cruzi-derived antigen: a mechanism of pathogenesis?

Trypanosoma cruzi can compromise the human central nervous system (CNS) during acute infection or reactivation in immune-suppressed hosts. Astrocytes have been identified as targets of T. cruzi's CNS infection in humans. Despite a high degree of parasitism and cellular lysis by T. cruzi in vitro the number of astrocytoma cells did not change when compared to uninfected cultures. This work evaluated cellular proliferation, changes in Major Histocompatibility Complex (MHC) expression as a reflection of antigen processing, and cytokine (IL-6 &amp; IL-8) secretion in a human astrocytoma cell line exposed to a trypomastigote-derived antigen. Light microscopy was used to evaluate the number of cells; MHC molecule expression, cell cycle and cytokine secretion were assessed by flow cytometry. The number of astrocytoma cells increased proportional to the amount of antigen used and the percentage of cells in G2/M phase was higher when compared to control cultures. Antigen exposure increased expression of MHC class II, but not MHC class I in comparison to cultures incubated without antigen. Astrocytoma cell secretion of IL-6 and IL-8 was unaffected by antigen exposure. These results suggest the participation of a trypomastigote-derived mediator that induces astrocytoma cell proliferation without an inflammatory response; which may contribute to the pathogenesis of neurologic Chagas disease.

Comparing preferences for outcomes of psoriasis treatments among patients and dermatologists in the U.K.: results from a discrete-choice experiment

BACKGROUND

Plaque psoriasis can have a significant negative effect on patients' quality of life, and treatments can result in serious toxicities. Although there have been several studies of patients' and physicians' relative preferences for the benefits and risks of psoriasis treatments, it is unclear how and whether patients' and physicians' preferences for the outcomes of psoriasis treatments differ.

OBJECTIVES

To quantify patient and dermatologist preferences for improvements in psoriasis symptoms and for increases in the risk of treatment-related serious adverse events.

METHODS

Members of the U.K. Psoriasis Association and U.K. dermatologists with experience prescribing biologics completed a web-enabled discrete-choice experiment survey in which they evaluated efficacy and safety features of biological treatments for psoriasis. Choices between hypothetical treatment options were used to estimate preference weights indicating respondents' relative trade-off preferences among treatment outcomes. These outcomes included improvements in the severity and coverage of psoriatic plaques and treatment-related risks of tuberculosis, serious infections and lymphoma. Preference estimates were used to derive the maximum level of side-effect risks that respondents would accept for improvements in psoriasis symptoms.

RESULTS

Respondents' tolerance for side-effect risks varied with side-effect severity and location of plaques, and risk tolerance for serious side-effects was greater for patients than for dermatologists.

CONCLUSIONS

Estimates of patients' risk tolerance for serious side-effects indicate that patients valued psoriasis symptom control highly and suggest that psoriasis symptoms have a significant effect on patients' quality of life. In light of research showing increased treatment satisfaction and improved treatment adherence among patients who receive therapies that are consistent with their preferences, our findings suggest that greater communication between dermatologists and patients about risk tolerance could help improve patient care.

Involvement of Tiam1, RhoG and ELMO2/ILK in Rac1-mediated phagocytosis in human trabecular meshwork cells

We previously demonstrated that an αvβ5 integrin/FAK- mediated pathway regulated the phagocytic properties of human trabecular meshwork (HTM) cells. Here we demonstrate that this process is mediated by Rac-1 and a previously unreported signaling pathway that utilizes the Tiam1 as well as a novel ILK/RhoG/ELMO2 signaling pathway. Phagocytosis in both a TM-1 cell line and normal HTM cells was mediated by Rac1 and could be significantly decreased by >75% using the Rac1 inhibitor EHop-016. Knockdown of Rac1 in TM-1 cells also inhibited phagocytosis by 40% whereas overexpression of a constitutively active Rac1 or stimulation with PDGF increased phagocytosis by 83% and 32% respectively. Tiam1 was involved in regulating phagocytosis. Knockdown of Tiam1 inhibited phagocytosis by 72% while overexpression of Tiam1 C1199 increased phagocytosis by 75%. Other upstream effectors of Rac1 found to be involved included ELMO2, RhoG, and ILK. Knockdowns of ELMO2, ILK, and RhoG caused a reduction in phagocytosis by 51%, 55% and 46% respectively. In contrast, knockdown of Vav2 and Dock1 or overexpression of Vav2 Y159/172F did not cause a significant change in phagocytosis. These data suggest a novel link between Tiam1 and RhoG/ILK /ELMO2 pathway as upstream effectors of the Rac1-mediated phagocytic process in TM cells.

Influence of dietary fat source and feeding duration on finishing pig growth performance, carcass composition, and fat quality

A total of 160 finishing pigs (PIC 327 × 1050; initially 45.6 kg) were used in an 84-d experiment to evaluate the effects of dietary fat source and feeding duration on growth performance, carcass characteristics, and carcass fat quality. There were 2 pigs per pen with 8 pens per treatment. The 10 dietary treatments were a corn-soybean meal control diet with no added fat and a 3 × 3 factorial with main effects of fat source (4% tallow, 4% soybean oil, or a blend of 2% tallow and 2% soybean oil) and feeding duration (d 0 to 42, 42 to 84, or 0 to 84). The control corn-soybean meal diet was fed in place of added fat diets when needed for duration treatment purposes. On d 0, 1 pig was identified in each pen and fat biopsy samples of the back, belly, and jowl were collected on d 0, 41, and 81 for fatty acid analysis. At the conclusion of the study, all pigs were harvested, carcass characteristics were determined, and back, belly, and jowl fat samples were collected for analysis. Overall (d 0 to 84), there were no differences among pigs fed the different fat sources for growth and carcass characteristics; however, pigs fed diets with added fat for the entire study had improved ( = 0.036) G:F compared with pigs fed the control diet without added fat. Pigs fed supplemental fat throughout the entire study also had improved ( < 0.05) ADG and G:F as well as heavier d-84 BW ( = 0.006) compared with pigs fed additional fat during only 1 period. Adding fat for the entire study increased ( = 0.032) backfat and tended to reduce ( = 0.079) the fat free lean index compared with pigs fed the control diet without added fat. Added fat also increased ( < 0.05) the iodine value (IV) when compared with pigs fed the control diet. Increasing the feeding duration of soybean oil lowered MUFA and increased PUFA concentrations for all fat depots, whereas these values remained relatively unchanged by the addition of tallow (duration × fat source interactions, < 0.05). Our study failed to show any feeding period × fat source interactions ( < 0.05) in fatty acid composition or IV for jowl fat, whereas this interaction occurred for belly fat and backfat, which would indicate a longer turnover rate for jowl fat. In conclusion, feeding additional fat improved ADG and G:F; however, feeding soybean oil for an increased duration, either alone or in combination with tallow, negatively affected the fatty acid composition and IV of different fat depots.

Toward in vivo two-photon analysis of mouse aqueous outflow structure and function

The promise of revolutionary insights into intraocular pressure (IOP) and aqueous humor outflow homeostasis, IOP pathogenesis, and novel therapy offered by engineered mouse models has been hindered by a lack of appropriate tools for studying the aqueous drainage tissues in their original 3-dimensional (3D) environment. Advances in 2-photon excitation fluorescence imaging (TPEF) combined with availability of modalities such as transgenic reporter mice and intravital dyes have placed us on the cusp of unlocking the potential of the mouse model for unearthing insights into aqueous drainage structure and function. Multimodality 2-photon imaging permits high-resolution visualization not only of tissue structural organization but also cells and cellular function. It is possible to dig deeper into understanding the cellular basis of aqueous outflow regulation as the technique integrates analysis of tissue structure, cell biology and physiology in a way that could also lead to fresh insights into human glaucoma. We outline recent novel applications of two-photon imaging to analyze the mouse conventional drainage system in vivo or in whole tissues: (1) collagen second harmonic generation (SHG) identifies the locations of episcleral vessels, intrascleral plexuses, collector channels, and Schlemm's canal in the distal aqueous drainage tract; (2) the prospero homeobox protein 1-green fluorescent protein (GFP) reporter helps locate the inner wall of Schlemm's canal; (3) Calcein AM, siGLO™, the fluorescent reporters m-Tomato and GFP, and coherent anti-Stokes scattering (CARS), are adjuncts to TPEF to identify live cells by their membrane or cytosolic locations; (4) autofluorescence and sulforhodamine-B to identify elastic fibers in the living eye. These tools greatly expand our options for analyzing physiological and pathological processes in the aqueous drainage tissues of live mice as a model of the analogous human system.

Optimizing two-photon multiple fluorophore imaging of the human trabecular meshwork

PURPOSE

Advances in two-photon (2P) deep tissue imaging provide powerful options for simultaneously viewing multiple fluorophores within tissues. We determined imaging parameters for optimally visualizing three fluorophores in the human trabecular meshwork (TM) to simultaneously detect broad-spectrum autofluorescence and multiple fluorophores through a limited number of emission filters.

METHODS

2P imaging of viable human postmortem TM was conducted to detect Hoechst 33342-labeled nuclei, Alexa-568-conjugated phalloidin labeling of filamentous actin, and autofluorescence of the structural extracellular matrix (ECM). Emission detection through green (500-550 nm), near-red (565-605 nm), and far-red (590-680 nm) filters following 2P excitation at 750, 800, 850, and 900 nm was analyzed. Region-of-interest (ROI) image analysis provided fluorescence intensity values for each fluorophore.

RESULTS

Red-channel Alexa 568 fluorescence was of highest intensity with 2P 750 nm and 800 nm excitation. Alexa 568 was imperceptible with 900 nm excitation. With excitation at 750 nm and 800 nm, Hoechst 33,342 intensity swamped autofluorescence in the green channel, and marked bleed-through into red channels was seen. 850 nm excitation yielded balanced Hoechst 33342 and autofluorescence intensities, minimized their bleed-through into the far-red channel, and produced reasonable Alexa 568 intensities in the far-red channel.

CONCLUSIONS

2P excitation at 850 nm and long-wavelength emission detection in the far-red channel allowed simultaneous visualization of the specific mix of endogenous and exogenous fluorophores with reasonably balanced intensities while minimizing bleed-through when imaging the human TM.

Dose- and time-dependent effects of actomyosin inhibition on live mouse outflow resistance and aqueous drainage tissues

Actomyosin contractility modulates outflow resistance of the aqueous drainage tissues and intraocular pressure, a key pathogenic factor of glaucoma. We established methodology to reliably analyze the effect of latrunculin-B (Lat-B)-induced actin depolymerization on outflow physiology in live mice. A voltage-controlled microperfusion system for delivering drugs and simultaneously analyzing outflow resistance was tested in live C57BL/6 mice. Flow rate and perfusion pressure were reproducible within a coefficient of variation of 2%. Outflow facility for phosphate-buffered saline (0.0027 ± 0.00036 μL/min/mmHg; mean ± SD) and 0.02% ethanol perfusions (Lat-B vehicle; 0.0023 ± 0.0005 μL/min/mmHg) were similar and stable over 2 hours (p > 0.1 for change), indicating absence of a ‘washout’ artifact seen in larger mammals. Outflow resistance changed in graded fashion, decreasing dose- and time-dependently over 2 hours for Lat-B doses of 2.5 μM (p = 0.29), 5 μM (p = 0.039) and 10 μM (p = 0.001). Resulting outflow resistance was about 10 times lower with 10 μM Lat-B than vehicle control. The filamentous actin network was decreased and structurally altered in the ciliary muscle (46 ± 5.6%) and trabecular meshwork (37 ± 8.3%) of treated eyes relative to vehicle controls (p < 0.005; 5 μM Lat-B). Mouse actomyosin contractile mechanisms are important to modulating aqueous outflow resistance, mirroring mechanisms in primates. We describe approaches to reliably probe these mechanisms in vivo.

Tissue-based multiphoton analysis of actomyosin and structural responses in human trabecular meshwork

The contractile trabecular meshwork (TM) modulates aqueous humor outflow resistance and intraocular pressure. The primary goal was to visualize and quantify human TM contractile state by analyzing actin polymerization (F-actin) by 2-photon excitation fluorescence imaging (TPEF) in situ. A secondary goal was to ascertain if structural extracellular matrix (ECM) configuration changed with contractility. Viable ex vivo human TM was incubated with latrunculin-A (Lat-A) or vehicle prior to Alexa-568-phalloidin labeling and TPEF. Quantitative image analysis was applied to 2-dimensional (2D) optical sections and 3D image reconstructions. After Lat-A exposure, (a) the F-actin network reorganized as aggregates; (b) F-actin-associated fluorescence intensity was reduced by 48.6% (mean; p = 0.007; n = 8); (c) F-actin 3D distribution was reduced by 68.9% (p = 0.040); (d) ECM pore cross-sectional area and volume were larger by 36% (p = 0.032) and 65% (p = 0.059) respectively and pores appeared more interconnected; (e) expression of type I collagen and elastin, key TM structural ECM proteins, were unaltered (p = 0.54); and (f) tissue viability was unchanged (p = 0.39) relative to vehicle controls. Thus Lat-A-induced reduction of actomyosin contractility was associated with TM porous expansion without evidence of reduced structural ECM protein expression or cellular viability. These important subcellular-level dynamics could be visualized and quantified within human tissue by TPEF.

Equations generated to predict iodine value of pork carcass back, belly, and jowl fat

Data from existing literature were used to generate equations to predict finishing pig back, belly, and jowl fat iodine values (IV) and an experiment was conducted to evaluate these equations. The final database included 24, 21, and 29 papers for back, belly, and jowl fat IV, respectively. For experiments that changed dietary fatty acid composition, initial (INT) diets were defined as those fed before the change in diet composition and final (FIN) diets were those fed after. The predictor variables tested were divided into 5 groups: 1) diet fat composition (dietary percent C16:1, C18:1, C18:2, C18:3, EFA, unsaturated fatty acids, and IV product) for both INT and FIN diets, 2) day feeding the INT and FIN diets, 3) ME or NE of the INT and FIN diet, 4) live performance criteria (initial BW, final BW, ADG, ADFI, and G:F), and 5) carcass criteria (HCW and backfat thickness). The PROC MIXED procedure of SAS (SAS Inst., Inc., Cary, NC) was used to develop regression equations. Evaluation of models with significant terms was then conducted based on the Bayesian information criterion. The optimum equations to predict back, belly, and jowl fat IV were backfat IV = 84.83 + (6.87 × INT EFA) - (3.90 × FIN EFA) - (0.12 × INT days) - (1.30 × FIN days) - (0.11 × INT EFA × FIN days) + (0.048 × FIN EFA × INT days) + (0.12 × FIN EFA × FIN days) - (0.0060 × FIN NE) + (0.0005 × FIN NE × FIN days) - (0.26 × backfat depth); belly fat IV = 106.16 + (6.21 × INT EFA) - (1.50 × FIN days) - (0.11 × INT EFA × FIN days) - (0.012 × INT NE) + (0.00069 × INT NE × FIN days) - (0.18 × HCW) - (0.25 × backfat depth); and jowl fat IV = 85.50 + (1.08 × INT EFA) + (0.87 × FIN EFA) - (0.014 × INT days) - (0.050 × FIN days) + (0.038 × INT EFA × INT days) + (0.054 × FIN EFA × FIN days) - (0.0066 × INT NE) + (0.071 × INT BW) - (2.19 × ADFI) - (0.29 × backfat depth). Dietary treatments from the evaluation experiment consisted of a corn-soybean meal control diet with no added fat or a 3 × 3 factorial arrangement with main effects of fat source (4% tallow, 4% soybean oil, or a blend of 2% tallow and 2% soybean oil) and feeding duration (d 0 to 42, 42 to 84, or 0 to 84). The back, belly, and jowl fat IV equations tended to overestimate IV when observed IV were less than approximately 65 g/100 g and underestimate belly fat IV when actual IV are greater than approximately 74 g/100 g or when the fat blend was fed from d 0 to 84 or 42 to 84. Overall, with the exceptions noted, the regression equations were an accurate tool for predicting carcass fat quality based on dietary and pig performance factors.

Effects of Added Zinc on Skeletal Muscle Morphometrics and Gene Expression of Finishing Pigs Fed Ractopamine-HCL

Finishing pigs (n = 320) were used in a 35-day study to determine the effects of ractopamine-HCl (RAC) and supplemental Zinc (Zn) level on loin eye area (LEA) and gene expression. Pens were randomly allotted to the following treatments for the final 35 days on feed: a corn-soybean meal diet (CON), a diet with 10 ppm RAC (RAC+), and RAC diet plus added Zn at 75, 150, or 225 ppm. Sixteen pigs per treatment were randomly selected for collection of serial muscle biopsies and carcass data on day 0, 8, 18, and 32 of the treatment phase. Compared to CON carcasses, RAC+ carcasses had 12.6% larger (P = 0.03) LEA. Carcasses from RAC diets with added Zn had a tendency for increased (quadratic, P < 0.10) LEA compared to the RAC+ carcasses. Compared to RAC+ pigs, relative expression of IGF1 decreased with increasing levels of Zn on day 8 and 18 of treatment, but expression levels were similar on day 32 due to Zn treatments increasing in expression while the RAC+ treatment decreased (Zn quadratic × day quadratic, P = 0.04). A similar trend was detected for the expression of β1-receptor where expression levels in the RAC+ pigs were greater than Zn supplemented pigs on day 8 and 18 of the experiment, but the magnitude of difference between the treatments was reduced on day 32 due to a decrease in expression by RAC+ pigs and an increase in expression by the Zn pigs (Zn quadratic × day quadratic, P = 0.01). The ability of Zn to prolong the expression of these two genes may be responsible for the tendency of Zn to increase LEA in RAC supplemented pigs.

Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity

Background

The Caldanaerobacter subterraneus species includes thermophilic fermentative bacteria able to grow on carbohydrates substrates with acetate and L-alanine as the main products. In this study, comprehensive analysis of three genomes of C. subterraneus subspecies was carried in order to identify genes encoding key metabolic enzymes and to document the genomic basis for the evolution of these organisms.

Methods

Average nucleotide identity and in silico DNA relatedness were estimated for the studied C. subterraneus genomes. Genome synteny was evaluated using R2CAT software. Protein conservation was analyzed using mGenome Subtractor. Horizontal gene transfer was predicted through the GOHTAM pipeline (using tetranucleotide composition) and phylogenetic analyses (by maximum likelihood). Hydrolases were identified through the MEROPS and CAZy platforms.

Results

The three genomes of C. subterraneus showed high similarity, although there are substantial differences in their gene composition and organization. Each subspecies possesses a gene cluster encoding a carbon monoxide dehydrogenase (CODH) and an energy converting hydrogenase (ECH). The CODH gene is associated with an operon that resembles the Escherichia coli hydrogenase hyc/hyf operons, a novel genetic context distinct from that found in archetypical hydrogenogenic carboxydotrophs. Apart from the CODH-associated hydrogenase, these bacteria also contain other hydrogenases, encoded by ech and hyd genes. An Mbx ferredoxin:NADP oxidoreductase homolog similar to that originally described in the archaeon Pyrococcus furiosus was uniquely encoded in the C. subterraneus subsp. yonseiensis genome. Compositional analysis demonstrated that some genes of the CODH-ECH and mbx operons present distinct sequence patterns in relation to the majority of the other genes of each genome. Phylogenetic reconstructions of the genes from these operons and those from the ech operon are incongruent to the species tree. Notably, the cooS gene of C. subterraneus subsp. pacificus and its homologs in C. subterraneus subsp. tengcongensis and C. subterraneus subsp. yonseiensis form distinct clades. The strains have diverse hydrolytic enzymes and they appear to be proteolytic and glycolytic. Divergent glycosidases from 14 families, among them amylases, chitinases, alpha-glucosidases, beta-glucosidases, and cellulases, were identified. Each of the three genomes also contains around 100 proteases from 50 subfamilies, as well about ten different esterases.

Conclusions

Genomic information suggests that multiple horizontal gene transfers conferred the adaptation of C. subterraneus subspecies to extreme niches throughout the carbon monoxide utilization and hydrogen production. The variety of hydrolases found in their genomes indicate the versatility of the species in obtaining energy and carbon from diverse substrates, therefore these organisms constitute a remarkable resource of enzymes with biotechnological potential.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1955-9) contains supplementary material, which is available to authorized users.

(123)I-FP-CIT SPECT imaging in early diagnosis of dementia in patients with and without a vascular component

Alzheimer’s disease (AD) and vascular dementia (VaD) are the most common cause of dementia. Cerebral ischemia is a major risk factor for development of dementia. ¹²³I-FP-CIT SPECT (DaTScan) is a complementary tool in the differential diagnoses of patients with incomplete or uncertain Parkinsonism. Additional application of DaTScan enables the categorization of Parkinsonian disease with dementia (PDD), and its differentiation from pure AD, and may further contribute to change the therapeutic decision. The aim of this study was to analyze the vascular contribution towards dementia and mild cognitive impairment (MCI). We evaluated the utility of DaTScan for the early diagnosis of dementia in patients with and without a clinical vascular component, and the association between neuropsychological function, vascular component and dopaminergic function on DaTScan. One-hundred and five patients with MCI or the initial phases of dementia were studied prospectively. We developed an initial assessment using neurologic examination, blood tests, cognitive function tests, structural neuroimaging and DaTScan. The vascular component was later quantified in two ways: clinically, according to the Framingham Risk Score (FRS) and by structural neuroimaging using Wahlund Scale Total Score (WSTS). Early diagnosis of dementia was associated with an abnormal DaTScan. A significant association was found between a high WSTS and an abnormal DaTScan (p < 0.01). Mixed AD was the group with the highest vascular component, followed by the VaD group, while MCI and pure AD showed similar WSTS. No significant associations were found between neuropsychological impairment and DaTScan independently of associated vascular component. DaTScan seems to be a good tool to discriminate, in a first clinical assessment, patients with MCI from those with established dementia. There was bigger general vascular affectation observable in MRI or CT in patients with abnormal dopaminergic uptake seen on DaTScan.

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

Background

A vast amount of DNA variation is being identified by increasingly large-scale exome and genome sequencing projects. To be useful, variants require accurate functional annotation and a wide range of tools are available to this end. McCarthy et al recently demonstrated the large differences in prediction of loss-of-function (LoF) variation when RefSeq and Ensembl transcripts are used for annotation, highlighting the importance of the reference transcripts on which variant functional annotation is based.

Results

We describe a detailed analysis of the similarities and differences between the gene and transcript annotation in the GENCODE and RefSeq genesets. We demonstrate that the GENCODE Comprehensive set is richer in alternative splicing, novel CDSs, novel exons and has higher genomic coverage than RefSeq, while the GENCODE Basic set is very similar to RefSeq. Using RNAseq data we show that exons and introns unique to one geneset are expressed at a similar level to those common to both. We present evidence that the differences in gene annotation lead to large differences in variant annotation where GENCODE and RefSeq are used as reference transcripts, although this is predominantly confined to non-coding transcripts and UTR sequence, with at most ~30% of LoF variants annotated discordantly. We also describe an investigation of dominant transcript expression, showing that it both supports the utility of the GENCODE Basic set in providing a smaller set of more highly expressed transcripts and provides a useful, biologically-relevant filter for further reducing the complexity of the transcriptome.

Conclusions

The reference transcripts selected for variant functional annotation do have a large effect on the outcome. The GENCODE Comprehensive transcripts contain more exons, have greater genomic coverage and capture many more variants than RefSeq in both genome and exome datasets, while the GENCODE Basic set shows a higher degree of concordance with RefSeq and has fewer unique features. We propose that the GENCODE Comprehensive set has great utility for the discovery of new variants with functional potential, while the GENCODE Basic set is more suitable for applications demanding less complex interpretation of functional variants.

Effects of the Programmed Nutrition Beef Program on feedlot performance and carcass characteristics

The objective of this study was to examine the effects of alternative finishing strategies on feedlot performance and carcass characteristics. Beef steers (64 pens; 8 steers/pen) were allocated to a randomized complete block design with a 2 × 2 factorial treatment arrangement. Factor 1 consisted of diet, with cattle fed a conventional (CON) diet or a diet consisting of Programmed Nutrition Beef Program (PN) supplements. The PN treatment included Programmed Nutrition Beef Receiver fed from d 1 through 20 of feeding and Programmed Nutrition Beef Finisher fed from d 21 to harvest. Factor 2 evaluated the presence (EGP+) or absence (EGP-) of exogenous growth promotants (ExGP) in the production system. Steers in the EGP+ treatments were initially implanted with Component E-S, reimplanted with Component TE-IS, and fed 400 mg·animal·dof ractopamine hydrochloride for the final 28 d before harvest. Steers were harvested on d 175, and strip loins were removed from 2 carcasses selected at random from each pen for transport to Kansas State University. One 1.27-cm-thick steak was removed from the anterior face for proximate and long-chain fatty acid analysis. There were no diet × ExGP interactions ( > 0.10) for feedlot performance except for DMI ( = 0.02). Steers in the PN/EGP+ treatment consumed more feed than all other treatments ( < 0.05). Both diet and ExGP affected DMI ( < 0.05), with PN and EGP+ steers consuming more feed than their contemporaries. Gain:feed and ADG were unaffected ( > 0.10) by diet, but ExGP improved these measures ( < 0.01). There were no diet × ExGP interactions for carcass characteristics except KPH fat and percentages of yield grade 3 and 4 carcasses ( < 0.05). Diet affected total incidence of liver abscesses because PN steers had a greater ( = 0.05) incidence of liver abscesses than steers in the CON treatment. Diet did not affect the other carcass characteristics ( > 0.10). Use of ExGP increased ( < 0.05) HCW, LM area, and 12th-rib fat but did not affect ( > 0.10) marbling score. Using ExGP reduced the percentage carcasses grading Premium Choice ( < 0.05). No diet × ExGP interactions or diet effects were detected for long-chain fatty acid profiles ( > 0.10). Use of ExGP increased ( < 0.05) the ratio of saturated:unsaturated fatty acids. In summary, the alternative feeding strategy presented in this study produced similar feedlot performance and carcass characteristics compared with a conventional feedlot system.

Mathematical Modeling of Different Molecule Removal on On-Line Haemodiafiltration: Influence of Dialysis Duration and Infusion Flow

BACKGROUND

In a previous study on a nocturnal, every-other-day online haemodiafiltration scheme, different removal patterns were observed for urea, creatinine, β2-​microglobulin, myoglobin and prolactin. The aim of this study was to evaluate the influence of dialysis duration and infusion flow (Qi) on the removal of different molecular weight (MW) solutes, and to quantify the effect of the different treatments on the kinetics of the solutes by using a classical two-compartment model.

METHODS

This prospective, in-center study was carried out in 10 patients on a nocturnal, every-other-day online post-dilution haemodiafiltration program. Each patient received four dialysis sessions with different conditions, two 4-h sessions (with infusion flows of 50 or 100 ml/min) and two 8-h sessions (with infusion flows of 50 or 100 ml/min). To analyze the solute kinetics, blood samples were obtained hourly during the dialysis treatments and in the first 3 h post-dialysis.

RESULTS

Removal patterns differed in the molecules studied, which were quantified by means of the two-compartment mathematical model. The main results show the impact of dialysis duration on the removal of low molecular weight molecules (urea and creatinine), while the impact of Qi is clearly shown for high molecular weight molecules (myoglobin and prolactin). For middle molecular weight solutes, such as β2-microglobulin, both factors (duration and Qi) enhance the removal efficiency of the dialyzer.

CONCLUSIONS

Our study evaluates experimentally and mathematically how treatment time and infusion flow affect the filtration of solutes of different MW during post-dilution haemodiafiltration. The results provided by the present study should help physicians to select and individualise the most appropriate schedules to deliver an optimum diffusive and convective dialysis dose for each patient.

Bacterial distribution along a 50 °C temperature gradient reveals a parceled out hot spring environment

Understanding the distribution of bacteria is a major goal of microbial ecology which remains to be fully deciphered. In this study, a model 50 °C temperature gradient at a Northern Thailand hot spring was analyzed to determine how the bacterial communities were structured in the environment. Communities were examined through 16S rRNA gene amplification, denaturing gradient gel electrophoresis, and sequencing. The two major phyla, Cyanobacteria and Chloroflexi, showed characteristic distributions along the temperature gradient. Different clades were allocated at specific portions of the gradient. Comparisons of the bacterial communities along the temperature gradient showed sharp decreases of similarity at increasing temperature difference. Peaks of maximum richness were observed at 50 and 70 °C. This study contributes to explain how environmental conditions and microbial interactions can influence the distribution of specific bacterial clades and phyla shaping the structure of microbial communities in nature.